Is it permissible for an accountant to take a cash amount from his trust and replace it with checks to pay the amount in installments, knowing that he was in financial distress?

What the company's regulations permit is the reference for determining what you are allowed and not allowed to do with its funds. If its regulations do not permit taking a sum of its cash and replacing it with checks, then you are not allowed to do so, as it involves violating its condition, unlawfully consuming people's wealth, and betraying trust. You must repent to Allah and return what you took to the company. However, if its regulations permit this, then there is no blame upon you.